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(-) Description

Title :  COMPLEX BETWEEN HUMAN SUMO2-RANGAP1, UBC9 AND ZNF451
 
Authors :  L. Cappadocia, C. D. Lima
Date :  05 Aug 15  (Deposition) - 04 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C,E,G  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Complex, Sumo, E3 Ligase, Ligase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cappadocia, A. Pichler, C. D. Lima
Structural Basis For Catalytic Activation By The Human Znf451 Sumo E3 Ligase.
Nat. Struct. Mol. Biol. V. 22 968 2015
PubMed-ID: 26524494  |  Reference-DOI: 10.1038/NSMB.3116

(-) Compounds

Molecule 1 - SUMO-CONJUGATING ENZYME UBC9
    Chains: A, D
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UBE2I, UBC9, UBCE9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUMO-PROTEIN LIGASE,UBIQUITIN CARRIER PROTEIN 9,UBIQUITIN CARRIER PROTEIN I,UBIQUITIN-CONJUGATING ENZYME E2 I,UBIQUITIN-PROTEIN LIGASE I,P18
 
Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER 2
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 15-93
    Gene: SUMO2, SMT3B, SMT3H2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUMO-2,HSMT3,SMT3 HOMOLOG 2,SUMO-3,SENTRIN-2,UBIQUITIN-LIKE PROTEIN SMT3B,SMT3B
 
Molecule 3 - RAN GTPASE-ACTIVATING PROTEIN 1
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSMT3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 418-587
    Gene: RANGAP1, KIAA1835, SD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RANGAP1
 
Molecule 4 - ZINC FINGER PROTEIN 451
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLOU3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-56
    Gene: ZNF451, COASTER, KIAA0576, KIAA1702
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COACTIVATOR FOR STEROID RECEPTORS

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): ABC E G
Biological Unit 2 (1x):    D F 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:18 , ASP A:19 , HOH A:432 , HOH A:434 , HOH A:471 , THR E:83 , ARG G:40binding site for residue EDO A 301
2AC2SOFTWAREGLY C:521binding site for residue EDO C 601
3AC3SOFTWARELYS C:481 , ASP C:482 , HOH C:764 , HIS D:20 , HOH D:265binding site for residue EDO C 602
4AC4SOFTWAREGLY F:521 , LEU F:522 , LYS F:524 , HOH F:713binding site for residue EDO F 601
5AC5SOFTWARETYR F:536 , CYS F:573 , SER F:574 , PHE F:575 , ALA F:576binding site for residue EDO F 602
6AC6SOFTWAREASN D:85 , CYS D:93 , ASP D:127 , PRO D:128 , ALA D:129 , HOH D:239 , GLY E:92 , LEU F:523 , SER F:525 , EDO F:601 , HOH F:707 , HOH F:785binding site for Di-peptide GLY E 93 and LYS F 524

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D2M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:68 -Pro A:69
2Glu A:78 -Pro A:79
3Tyr D:68 -Pro D:69
4Glu D:78 -Pro D:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D2M)

(-) Exons   (0, 0)

(no "Exon" information available for 5D2M)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eeee................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d2m A   1 MSGIALSRLAQERRAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAP 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeee......hhhhhhhhhhhhh.....eeeee..ee...............eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5d2m B  18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  93
                                    27        37        47        57        67        77        87      


Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..............hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d2m C 430 PPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV 587
                                   439       449       459       469       479       489       499       509       519       529       539       549       559       569       579        


Chain D from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eeee................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d2m D   1 MSGIALSRLAQERRAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAP 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain E from PDB  Type:PROTEIN  Length:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee...............eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 5d2m E  14 MNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  93
                                    23        33        43        53        63        73        83        93


Chain F from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d2m F 431 PADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV 587
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       


Chain G from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 5d2m G  30 DIQFVSEGPLRPVLEYIDLVS  50
                                    39        49
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5D2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D2M)

(-) Gene Ontology  (70, 90)

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  SUMO2_HUMAN | P61956
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  UBC9_HUMAN | P63279
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  ZN451_HUMAN | Q9Y4E5
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RAGP1_HUMAN | P46060: 1z5s 2grn 2gro 2grp 2grq 2grr 2io2 2io3 2iy0 3uin 3uio 3uip
        SUMO2_HUMAN | P61956: 1wm2 1wm3 1wz0 1z5q 2awt 2ckh 2d07 2io0 2io3 2iyd 2n1w 2n9e 2rpq 3uin 3uio 3zo5 4bkg 4npn 5elu 5eql 5ghb 5ghc
        UBC9_HUMAN | P63279: 1a3s 1kps 1z5q 1z5s 2grn 2gro 2grp 2grq 2grr 2o25 2pe6 2px9 2xwu 3a4s 3uin 3uio 3uip 4w5v 4y1l 5f6d 5f6e 5f6u 5f6v 5f6w 5f6x 5f6y 5fq2

(-) Related Entries Specified in the PDB File

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